May 2021 - ChimeraX-users - RBVI Mailing Lists

Release of ISOLDE 1.2
by Tristan Croll 13 May '21

13 May '21

Hi all, I'm very happy to announce the release of ISOLDE 1.2, now available for installation into the ChimeraX 1.2 release. To get it, first download and install ChimeraX 1.2 from https://www.rbvi.ucsf.edu/chimerax/download.html, then go to "Tools/More Tools..." in the menu and follow the links to install ISOLDE. Key new features include: * The ability to add residues to the ends of protein chains (see https://twitter.com/CrollTristan/status/1391747032579289089?s=20; support for nucleic acid chain extension still in development) * Lower-fidelity simulation modes for greatly improved performance on lower-end GPUs (see https://twitter.com/CrollTristan/status/1390709520876331009?s=20) * Commands to write input files for phenix.refine and phenix.real_space_refine with recommended settings for refining models from ISOLDE * Command to write a ProSMART-like restraint definition file to softly restrain the model to its current geometry in Refmac * Improvements to stability and performance of bulk solvent/scaling in crystallographic datasets * Short aliases for commonly-used commands to make life easier for power users. Please enjoy! Best regards, Tristan

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BLAST fix
by Eric Pettersen 12 May '21

12 May '21

Hi all, The RCSB switching off http access and only allowing https (which had been announced) unfortunately broke the fetching of PDB info associated with BLAST results, basically breaking the BLAST tools in both Chimera and ChimeraX. Fixes have been applied and will be available in tomorrow's daily builds. For ChimeraX, also available in the 1.2.3 release candidate -- hopefully also out tomorrow. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Generating map from structure
by Eric Pettersen 11 May '21

11 May '21

> Begin forwarded message: > > From: "Azad, Roksana" <razad(a)gc.cuny.edu> > Subject: Re: [ChimeraX] #4622: save dialog: 'SaveModelOptionWidget' object has no attribute '_name' > Date: May 11, 2021 at 9:00:00 AM PDT > To: "ChimeraX-bugs(a)cgl.ucsf.edu" <ChimeraX-bugs(a)cgl.ucsf.edu> > > Dear Eric, > Thank you so much for your reply. > > I have a model of my protein in pdb format, which I am trying to save as .mrc or any sort of volume file on chimera. However, since its a model and do not have any coordinate in the file like xtal or NMR structure, it won’t save it as .mrc or volume file and was giving me the error. > > I want to create a volume file from the model to load on cryoSPARC or relion and create 2D projections to help me pick better 2D classes from my raw data. Do you think there is an option to do something like this on chimera? > > Thank you again for your time and help in advance – very much appreciated. > > Sincerely, > Roksana > >> On May 11, 2021, at 11:50 AM, ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> wrote: >> >> #4622: save dialog: 'SaveModelOptionWidget' object has no attribute '_name' >> -----------------------------------+---------------------------- >> Reporter: razad@… | Owner: Eric Pettersen >> Type: defect | Status: closed >> Priority: normal | Milestone: >> Component: Input/Output | Version: >> Resolution: duplicate | Keywords: >> Blocked By: | Blocking: >> Notify when closed: | Platform: all >> Project: ChimeraX | >> -----------------------------------+---------------------------- >> Changes (by Eric Pettersen): >> >> * status: accepted => closed >> * resolution: => duplicate >> >> >> Comment: >> >> Hi Roksana, >> Thanks for reporting this problem. ChimeraX was trying to tell >> you that you hadn't selected anything to save in the save dialog, but >> there was an error in the code that generates that message, which is what >> you saw. So the error is easy to avoid. Nonetheless, if you want to >> always avoid it in the future you could use the current daily build or the >> 1.2.2 release candidate, both of which have this problem fixed. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> -- >> Ticket URL: <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_tra… > >> ChimeraX <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.rbvi.ucsf.edu_chime… > >> ChimeraX Issue Tracker > >

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job opening for ChimeraX developer
by Elaine Meng 06 May '21

06 May '21

Hello everybody, We're looking for somebody to join the ChimeraX development team! Please see this posting for details: <https://sjobs.brassring.com/TGnewUI/Search/Home/Home?partnerid=6495&siteid=…> On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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DAE format
by Giorgio Luciano 06 May '21

06 May '21

Hello to all, I'm writing for a feature request. The old chimera had the option to export models (surfaces, ball and stickers etc) in DAE format which is the most "trustful" for importing the model in 3D software (blender for me now). Will it be possible to "revamp" it or include format as .abc ? (I don't know if .usd can be an idea also since I think its specifications are open). Thanks

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ChimeraX not starting up using win10
by Bernd M. Schmidt 05 May '21

05 May '21

Dear ChimeraX users and coders, Thanks for the hard work and for providing the community with such great program. I cannot run Chimera on my desktop PC. After clicking in win10, the cursor indicates something is happening for three seconds, then nothing happens and also no error message or anything appeares Before that, I ran Chimera 1.14rc successfully, since installation of ChimeraX and also with ChimeraX 1.2, this happens. I deinstalled everything and installed first the latest python release (3.9.5), then ChimeraX 1.2. But no change, nothing. Reading the newsgroup suggested running debug mode, finally giving some error message, as seen below. C:\Program Files\ChimeraX 1.2\bin\lib\site-packages\win32\lib\pywintypes.py:2: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses import imp, sys, os Windows fatal exception: access violation Current thread 0x000023f8 (most recent call first): File "C:\Program Files\ChimeraX 1.2\bin\lib\site-packages\chimerax\ui\gui.py", line 157 in __init__ File "C:\Program Files\ChimeraX 1.2\bin\lib\site-packages\ChimeraX_main.py", line 577 in init File "C:\Program Files\ChimeraX 1.2\bin\lib\site-packages\ChimeraX_main.py", line 1015 in <module> File "C:\Program Files\ChimeraX 1.2\bin\lib\runpy.py", line 87 in _run_code File "C:\Program Files\ChimeraX 1.2\bin\lib\runpy.py", line 194 in _run_module_as_main C:\Program Files\ChimeraX 1.2\bin> Happy for some help. Many greetings bernd

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Saving name attribute
by David Leeming 04 May '21

04 May '21

Hi, I'm attempting to use a python script to save the names of each residue in a protein The code I have is as follows: import chimerax, sys from chimerax.core.commands import run cwd = (str(sys.argv[0][:-17])) prot = "/A" run(session, "open 3GDM") run(session, "save " + str(cwd) + "/script_content/sasa/name.defattr " + str(prot) + " & protein attrName r:name format defattr") The command being input into the command line of ChimeraX by the script is as follows: "save [file path]/name.defattr /A & protein attrName r:name format defattr" I've also tried using: "save [file path]/name.defattr attrName r:name format defattr models /A & protein" However, both commands give me a file with all the residues and all the names contained within the model rather than just the chain I'm interested in. Could you advise on how I can better use this command to save a file with the residue positions and corresponding amino acid for each residue from a single chain only? I've attached the resultant file to this email. Kind regards, David

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assigning 3.10 helices to a pdb
by Sheena Vasquez 03 May '21

03 May '21

Hi everyone, I was wondering if there's a way to reassign alpha-helices to 3.10 helices in chimeraX? I've been using the setattr /A:###-### res ss_type 1 command, but it seems as if there's only the option to assign alpha helices (ss_type 1). If I try ss_type 5 (5 is the assigned number for 3.10 helices in the pdb), the helix is lost. Any help with this is greatly appreciated! Take care, Sheena

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ChimeraX-users May 2021